He studied philosophy at the University of Athens, then Byzantine history at the Sorbonne in Charles Diehl. On his return to Athens, he was from 1937 to 1946 director of the Greek State Archives. From 1939 to 1970 he was Professor of Byzantine History at the University of Athens. 1951-1965 is a professor of history of modern Greek civilization and politics at Panteios. 1966 Zakythinos was a member of the Academy of Athens, at times he was its president. For his scientific work Zakythinos has received numerous national and international awards. In 1974 he was elected to the Greek Parliament and was Minister until 1977.
He was one of the founders of the Association Internationale des Etudes Byzantines, from 1961 to 1971 its general secretary, from 1971 to 1976 its president.